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Sandoval-Talamantes AK, Tenorio-Castaño JA, Santos-Simarro F, Adán C, Fernández-Elvira M, García-Fernández L, Muñoz Y, Lapunzina P, Nevado J. NGS Custom Panel Implementation in Patients with Non-Syndromic Autism Spectrum Disorders in the Clinical Routine of a Tertiary Hospital. Genes (Basel) 2023; 14:2091. [PMID: 38003033 PMCID: PMC10671584 DOI: 10.3390/genes14112091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Autism spectrum disorder (ASD) is a set of neurodevelopmental disorders characterized by deficiencies in communication, social interaction, and repetitive and restrictive behaviors. The discovery of genetic involvement in the etiology of ASD has made this condition a strong candidate for genome-based diagnostic tests. Next-generation sequencing (NGS) is useful for the detection of variants in the sequence of different genes in ASD patients. Herein, we present the implementation of a personalized NGS panel for autism (AutismSeq) for patients with essential ASD over a prospective period of four years in the clinical routine of a tertiary hospital. The cohort is composed of 48 individuals, older than 3 years, who met the DSM-5 (The Diagnostic and Statistical Manual of Mental Disorders) diagnostic criteria for ASD. The NGS customized panel (AutismSeq) turned out to be a tool with good diagnostic efficacy in routine clinical care, where we detected 12 "pathogenic" (including pathogenic, likely pathogenic, and VUS (variant of uncertain significance) possibly pathogenic variations) in 11 individuals, and 11 VUS in 10 individuals, which had previously been negative for chromosomal microarray analysis and other previous genetic studies, such as karyotype, fragile-X, or MLPA/FISH (Multiplex Ligation dependent Probe Amplification/Fluorescence in situ hybridization) analysis. Our results demonstrate the high genetic and clinical heterogeneity of individuals with ASD and the current difficulty of molecular diagnosis. Our study also shows that an NGS-customized panel might be useful for diagnosing patients with essential/primary autism and that it is cost-effective for most genetic laboratories.
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Affiliation(s)
- Ana Karen Sandoval-Talamantes
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
| | - Jair Antonio Tenorio-Castaño
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
- ITHACA, European Research Network, La Paz University Hospital, 28046 Madrid, Spain
- CIBERER (Network for Biomedical Research on Rare Diseases), Carlos III Health Institute (ISCIII), 28046 Madrid, Spain
| | - Fernando Santos-Simarro
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
- ITHACA, European Research Network, La Paz University Hospital, 28046 Madrid, Spain
- CIBERER (Network for Biomedical Research on Rare Diseases), Carlos III Health Institute (ISCIII), 28046 Madrid, Spain
| | - Carmen Adán
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
| | - María Fernández-Elvira
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
| | - Laura García-Fernández
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
| | - Yolanda Muñoz
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
| | - Pablo Lapunzina
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
- ITHACA, European Research Network, La Paz University Hospital, 28046 Madrid, Spain
- CIBERER (Network for Biomedical Research on Rare Diseases), Carlos III Health Institute (ISCIII), 28046 Madrid, Spain
| | - Julián Nevado
- INGEMM (Institute of Medical and Molecular Genetics), La Paz University Hospital, IdiPAZ, 28046 Madrid, Spain; (A.K.S.-T.); (J.A.T.-C.); (F.S.-S.); (C.A.); (M.F.-E.); (L.G.-F.); (Y.M.); (P.L.)
- ITHACA, European Research Network, La Paz University Hospital, 28046 Madrid, Spain
- CIBERER (Network for Biomedical Research on Rare Diseases), Carlos III Health Institute (ISCIII), 28046 Madrid, Spain
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Sandoval-Talamantes AK, Mori MÁ, Santos-Simarro F, García-Miñaur S, Mansilla E, Tenorio JA, Peña C, Adan C, Fernández-Elvira M, Rueda I, Lapunzina P, Nevado J. Chromosomal Microarray in Patients with Non-Syndromic Autism Spectrum Disorders in the Clinical Routine of a Tertiary Hospital. Genes (Basel) 2023; 14:genes14040820. [PMID: 37107578 PMCID: PMC10137620 DOI: 10.3390/genes14040820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Autism spectrum disorders (ASD) comprise a group of neurodevelopmental disorders (NDD) characterized by deficits in communication and social interaction, as well as repetitive and restrictive behaviors, etc. The genetic implications of ASD have been widely documented, and numerous genes have been associated with it. The use of chromosomal microarray analysis (CMA) has proven to be a rapid and effective method for detecting both small and large deletions and duplications associated with ASD. In this article, we present the implementation of CMA as a first-tier test in our clinical laboratory for patients with primary ASD over a prospective period of four years. The cohort was composed of 212 individuals over 3 years of age, who met DSM-5 diagnostic criteria for ASD. The use of a customized array-CGH (comparative genomic hybridization) design (KaryoArray®) found 99 individuals (45.20%) with copy number variants (CNVs); 34 of them carried deletions (34.34%) and 65 duplications (65.65%). A total of 28 of 212 patients had pathogenic or likely pathogenic CNVs, representing approximately 13% of the cohort. In turn, 28 out of 212 (approximately 12%) had variants of uncertain clinical significance (VUS). Our findings involve clinically significant CNVs, known to cause ASD (syndromic and non-syndromic), and other CNVs previously related to other comorbidities such as epilepsy or intellectual disability (ID). Lastly, we observed new rearrangements that will enhance the information available and the collection of genes associated with this disorder. Our data also highlight that CMA could be very useful in diagnosing patients with essential/primary autism, and demonstrate the existence of substantial genetic and clinical heterogeneity in non-syndromic ASD individuals, underscoring the continued challenge for genetic laboratories in terms of its molecular diagnosis.
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Rodríguez-Contreras FJ, Marbán-Calzón M, Vallespín E, Del Pozo Á, Solís-López M, Lobato-Vidal N, Fernández-Elvira M, Del Valle Rex-Romero M, Heath KE, González-Casado I, Campos-Barros Á. Loss of function BMP4 mutation supports the implication of the BMP/TGF-β pathway in the etiology of combined pituitary hormone deficiency. Am J Med Genet A 2019; 179:1591-1597. [PMID: 31120642 DOI: 10.1002/ajmg.a.61201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/19/2022]
Abstract
Despite BMP4 signaling being critical to Rathke's pouch induction and maintenance during early stages of pituitary development, its implication in the etiology of combined pituitary hormone deficiency (CPHD) and other clinical presentations of congenital hypopituitarism has not yet been definitely demonstrated. We report here the first CPHD patient with a de novo pathogenic loss-of-function variant in BMP4. A 6-year-old boy, with macrocephaly, myopia/astigmatism, mild psychomotor retardation, anterior pituitary hypoplasia and ectopic posterior pituitary, clinically diagnosed with growth hormone deficiency, and central hypothyroidism, was referred for genetic analysis of CPHD. Targeted NGS analysis with a custom panel (n = 310 genes) identified a novel heterozygous de novo nonsense variant, NM_001202.5:c.794G > A, p.(Trp265*) in BMP4, which introduces a premature stop codon in the BMP4 pro-domain, impairing the transcription of the TGF-β mature peptide domain. Additional relevant variants in other genes implicated in pituitary development signaling pathways such as SMAD4 and E2F4 (BMP/TGF-pathway), ALMS1 (NOTCH-pathway), and TSHZ1 (Prokineticin-pathway), were also identified. Our results support the implication of the BMP/TGF-β signaling pathway in the etiology of CPHD and suggest that oligogenic contribution of additional inherited variants may modify the phenotypic expressivity of BMP4 pathogenic variants.
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Affiliation(s)
- Francisco J Rodríguez-Contreras
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Department of Pediatrics, Centro de Salud Galapagar, Madrid, Spain
| | | | - Elena Vallespín
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | - Ángela Del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario Solís-López
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - Nerea Lobato-Vidal
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - María Fernández-Elvira
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - María Del Valle Rex-Romero
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
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